library(topGO)
library(stats)
library(knitr)
setwd('/Users/mmayers/projects/n15_mice/data/')
data.dir <- '../data'
gene2GOID <- readMappings('clusterID2GO.map')
unenr_pvals <- read.csv(file.path(data.dir, 'unenriched_pvals.csv'))
unenr_pvals$log2FoldChange <- log2(unenr_pvals$ratio)
unenr_pvals$padj <- p.adjust(unenr_pvals$p_value, method="BH")
GO2geneMF <- annFUN.gene2GO('MF', gene2GO=gene2GOID)
GO2geneBP <- annFUN.gene2GO('BP', gene2GO=gene2GOID)
do some stuff with fold changes
unenr_pvals$adjFC <- unenr_pvals$log2FoldChange
n <- sum(unenr_pvals$padj > .05 & abs(unenr_pvals$log2FoldChange) > 2)
unenr_pvals[unenr_pvals$padj > .05 & abs(unenr_pvals$log2FoldChange) > 2, ]$adjFC <- rep(0, n)
#set.seed(2222)
#unenr_pvals[unenr_pvals$padj > .05 & abs(unenr_pvals$log2FoldChange) > 2, ]$adjFC <- runif(n, -1, 1)
hist(unenr_pvals$log2FoldChange, 15)

hist(unenr_pvals$adjFC, 15)

Look at Bacterial Proteins only
Mouse Human subset seems to be a bust, can’t figure out good way to account for tiny background)
tmp <- locusTable$mouse_human == 'False' & locusTable$lca != '35823' # Filtering out anthrospira differences 35823
tmp[is.na(tmp)] <- TRUE
bac.prots <- locusTable[tmp, ]$X
bac.pvals <- unenr_pvals[unenr_pvals$X %in% bac.prots, ]
geneList.bac <- bac.pvals$padj
geneList.bac <- bac.pvals$adjFC
names(geneList.bac) <- bac.pvals$X
topDiffGenes <- function(score) {return(score >= 2)} # scoring function, anything with > 2 logfc is sig anyway
TCell vs RAG - Unenriched
geneList.bac <- -1*geneList.bac
MF first
ontology <- 'MF'
GOdata.bac <- new('topGOdata', ontology = ontology, allGenes = geneList.bac, geneSel = topDiffGenes, annot = annFUN.gene2GO, gene2GO = gene2GOID)
result.bac.ks <- runTest(GOdata.bac, statistic = 'ks')
a <- GenTable(GOdata.bac, result.bac.ks, topNodes = 10)
kable(a)
| GO:0004619 |
phosphoglycerate mutase activity |
42 |
0 |
4.77 |
1.4e-26 |
| GO:0000287 |
magnesium ion binding |
46 |
0 |
5.23 |
8.6e-09 |
| GO:0005506 |
iron ion binding |
80 |
0 |
9.09 |
7.2e-07 |
| GO:0016491 |
oxidoreductase activity |
291 |
15 |
33.07 |
1.3e-06 |
| GO:0008184 |
glycogen phosphorylase activity |
14 |
0 |
1.59 |
1.6e-06 |
| GO:0004634 |
phosphopyruvate hydratase activity |
34 |
0 |
3.86 |
5.0e-06 |
| GO:0046933 |
proton-transporting ATP synthase activit… |
14 |
1 |
1.59 |
4.1e-05 |
| GO:0016639 |
oxidoreductase activity, acting on the C… |
29 |
0 |
3.30 |
4.3e-05 |
| GO:0004618 |
phosphoglycerate kinase activity |
27 |
3 |
3.07 |
6.3e-05 |
| GO:0003677 |
DNA binding |
61 |
0 |
6.93 |
6.8e-05 |
for (term in a$GO.ID){
print(a[a$GO.ID == term, ]$Term)
print(showGroupDensity(GOdata.bac, term, ranks=TRUE))
}
## [1] "phosphoglycerate mutase activity"

## [1] "magnesium ion binding"

## [1] "iron ion binding"

## [1] "oxidoreductase activity"

## [1] "glycogen phosphorylase activity"

## [1] "phosphopyruvate hydratase activity"

## [1] "proton-transporting ATP synthase activit..."

## [1] "oxidoreductase activity, acting on the C..."

## [1] "phosphoglycerate kinase activity"

## [1] "DNA binding"

#showGroupDensity(GOdata.bac, "GO:0008184", ranks=TRUE) #Glycogen phosphorlase
#showGroupDensity(GOdata.bac, "GO:0004618", ranks=TRUE) #phosphoglycerate kinase
ontology <- 'BP'
BP - Tcell vs RAG: Unenriched
GOdata.bac <- new('topGOdata', ontology = ontology, allGenes = geneList.bac, geneSel = topDiffGenes, annot = annFUN.gene2GO, gene2GO = gene2GOID)
result.bac.ks <- runTest(GOdata.bac, statistic = 'ks')
a <- GenTable(GOdata.bac, result.bac.ks, topNodes = 10)
kable(a)
| GO:0006096 |
glycolytic process |
148 |
25 |
15.31 |
2.3e-18 |
| GO:0005975 |
carbohydrate metabolic process |
320 |
48 |
33.11 |
4.0e-14 |
| GO:0008152 |
metabolic process |
1017 |
92 |
105.24 |
2.1e-06 |
| GO:0055114 |
oxidation-reduction process |
312 |
28 |
32.29 |
1.8e-05 |
| GO:0015986 |
ATP synthesis coupled proton transport |
15 |
1 |
1.55 |
0.00028 |
| GO:0006520 |
cellular amino acid metabolic process |
78 |
0 |
8.07 |
0.00031 |
| GO:0006108 |
malate metabolic process |
6 |
0 |
0.62 |
0.00037 |
| GO:0008654 |
phospholipid biosynthetic process |
13 |
0 |
1.35 |
0.00072 |
| GO:0006021 |
inositol biosynthetic process |
13 |
0 |
1.35 |
0.00072 |
| GO:0006351 |
transcription, DNA-templated |
63 |
0 |
6.52 |
0.00077 |
for (term in a$GO.ID){
print(a[a$GO.ID == term, ]$Term)
print(showGroupDensity(GOdata.bac, term, ranks=TRUE))
}
## [1] "glycolytic process"

## [1] "carbohydrate metabolic process"

## [1] "metabolic process"

## [1] "oxidation-reduction process"

## [1] "ATP synthesis coupled proton transport"

## [1] "cellular amino acid metabolic process"

## [1] "malate metabolic process"

## [1] "phospholipid biosynthetic process"

## [1] "inositol biosynthetic process"

## [1] "transcription, DNA-templated"

#showGroupDensity(GOdata.bac, "GO:0006096", ranks=TRUE) # Glycolitc Process
#showGroupDensity(GOdata.bac, "GO:0005975", ranks=TRUE) # Carbohydydrate metab
# Mostly Carb metabolism? lipid biosynthesis?Nah, those look crappy
RAG vs Tcell - Unenriched
geneList.bac <- -1*geneList.bac
MF
ontology <- 'MF'
GOdata.bac <- new('topGOdata', ontology = ontology, allGenes = geneList.bac, geneSel = topDiffGenes, annot = annFUN.gene2GO, gene2GO = gene2GOID)
result.bac.ks <- runTest(GOdata.bac, statistic = 'ks')
a <- GenTable(GOdata.bac, result.bac.ks, topNodes = 10)
kable(a)
| GO:0005524 |
ATP binding |
233 |
2 |
4.38 |
1.7e-24 |
| GO:0003872 |
6-phosphofructokinase activity |
25 |
0 |
0.47 |
1.8e-14 |
| GO:0004478 |
methionine adenosyltransferase activity |
29 |
0 |
0.55 |
8.1e-13 |
| GO:0005198 |
structural molecule activity |
151 |
0 |
2.84 |
5.5e-12 |
| GO:0050242 |
pyruvate, phosphate dikinase activity |
74 |
0 |
1.39 |
6.9e-12 |
| GO:0016887 |
ATPase activity |
34 |
0 |
0.64 |
2.5e-11 |
| GO:0008878 |
glucose-1-phosphate adenylyltransferase … |
15 |
0 |
0.28 |
7.0e-11 |
| GO:0016301 |
kinase activity |
128 |
1 |
2.41 |
5.3e-09 |
| GO:0003924 |
GTPase activity |
77 |
1 |
1.45 |
4.1e-08 |
| GO:0003824 |
catalytic activity |
1023 |
22 |
19.24 |
1.7e-06 |
for (term in a$GO.ID){
print(a[a$GO.ID == term, ]$Term)
print(showGroupDensity(GOdata.bac, term, ranks=TRUE))
}
## [1] "ATP binding"

## [1] "6-phosphofructokinase activity"

## [1] "methionine adenosyltransferase activity"

## [1] "structural molecule activity"

## [1] "pyruvate, phosphate dikinase activity"

## [1] "ATPase activity"

## [1] "glucose-1-phosphate adenylyltransferase ..."

## [1] "kinase activity"

## [1] "GTPase activity"

## [1] "catalytic activity"

BP - RAG vs Tcell: Unenriched
ontology <- 'BP'
GOdata.bac <- new('topGOdata', ontology = ontology, allGenes = geneList.bac, geneSel = topDiffGenes, annot = annFUN.gene2GO, gene2GO = gene2GOID)
result.bac.ks <- runTest(GOdata.bac, statistic = 'ks')
a <- GenTable(GOdata.bac, result.bac.ks, topNodes = 10)
kable(a)
| GO:0006556 |
S-adenosylmethionine biosynthetic proces… |
29 |
0 |
0.48 |
6.8e-14 |
| GO:0071973 |
bacterial-type flagellum-dependent cell … |
95 |
0 |
1.57 |
3.8e-13 |
| GO:0006002 |
fructose 6-phosphate metabolic process |
22 |
0 |
0.36 |
7.4e-13 |
| GO:0006090 |
pyruvate metabolic process |
222 |
0 |
3.67 |
1.1e-12 |
| GO:0016310 |
phosphorylation |
229 |
1 |
3.78 |
1.2e-12 |
| GO:0005978 |
glycogen biosynthetic process |
15 |
0 |
0.25 |
4.1e-11 |
| GO:0009401 |
phosphoenolpyruvate-dependent sugar phos… |
13 |
0 |
0.21 |
4.6e-07 |
| GO:0044267 |
cellular protein metabolic process |
130 |
2 |
2.15 |
1.1e-06 |
| GO:0006810 |
transport |
61 |
0 |
1.01 |
4.0e-06 |
| GO:0055114 |
oxidation-reduction process |
312 |
4 |
5.15 |
4.6e-05 |
for (term in a$GO.ID){
print(a[a$GO.ID == term, ]$Term)
print(showGroupDensity(GOdata.bac, term, ranks=TRUE))
}
## [1] "S-adenosylmethionine biosynthetic proces..."

## [1] "bacterial-type flagellum-dependent cell ..."

## [1] "fructose 6-phosphate metabolic process"

## [1] "pyruvate metabolic process"

## [1] "phosphorylation"

## [1] "glycogen biosynthetic process"

## [1] "phosphoenolpyruvate-dependent sugar phos..."

## [1] "cellular protein metabolic process"

## [1] "transport"

## [1] "oxidation-reduction process"

BioGlyCMK Rag vs Tcell
enr_pvals <- read.csv(file.path(data.dir, 'enriched_pvals.csv'))
enr_pvals$log2FoldChange <- log2(enr_pvals$ratio)
enr_pvals$padj <- p.adjust(enr_pvals$p_value, method="BH")
Fix fold change of insignifcant proteins
enr_pvals$adjFC <- enr_pvals$log2FoldChange
n <- sum(enr_pvals$padj > .05 & abs(enr_pvals$log2FoldChange) > 2)
#set.seed(1234)
#enr_pvals[enr_pvals$padj > .05 & abs(enr_pvals$log2FoldChange) > 2, ]$adjFC <- runif(n, -1, 1)
enr_pvals[enr_pvals$padj > .05 & abs(enr_pvals$log2FoldChange) > 2, ]$adjFC <- rep(0, n)
hist(enr_pvals$log2FoldChange, 15)

hist(enr_pvals$adjFC, 15)

Bacterial proteins only
bac.enr.pvals <- enr_pvals[enr_pvals$X %in% bac.prots, ]
#geneList.bac <- bac.pvals$padj
geneList.bac.enr <- bac.enr.pvals$adjFC
names(geneList.bac.enr) <- bac.enr.pvals$X
Tcell vs RAG - Enriched
geneList.bac.enr <- -1*geneList.bac.enr # KS goes from - to +
# do this to put upreg in Tcell first
MF
ontology <- 'MF'
GOdata.bac.enr <- new('topGOdata', ontology = ontology, allGenes = geneList.bac.enr, geneSel = topDiffGenes, annot = annFUN.gene2GO, gene2GO = gene2GOID)
result.bac.enr.ks <- runTest(GOdata.bac.enr, statistic = 'ks')
a <- GenTable(GOdata.bac.enr, result.bac.enr.ks, topNodes = 10)
kable(a)
| GO:0016639 |
oxidoreductase activity, acting on the C… |
70 |
0 |
0.45 |
2.5e-07 |
| GO:0016491 |
oxidoreductase activity |
367 |
2 |
2.36 |
6.1e-07 |
| GO:0016829 |
lyase activity |
160 |
1 |
1.03 |
1.2e-06 |
| GO:0051287 |
NAD binding |
22 |
0 |
0.14 |
5.1e-06 |
| GO:0016462 |
pyrophosphatase activity |
50 |
0 |
0.32 |
6.6e-06 |
| GO:0050661 |
NADP binding |
20 |
0 |
0.13 |
9.4e-06 |
| GO:0005515 |
protein binding |
16 |
0 |
0.10 |
0.00020 |
| GO:0005215 |
transporter activity |
25 |
0 |
0.16 |
0.00025 |
| GO:0004197 |
cysteine-type endopeptidase activity |
7 |
0 |
0.04 |
0.00135 |
| GO:0005506 |
iron ion binding |
52 |
0 |
0.33 |
0.00155 |
for (term in a$GO.ID){
print(a[a$GO.ID == term, ]$Term)
print(showGroupDensity(GOdata.bac.enr, term, ranks=TRUE))
}
## [1] "oxidoreductase activity, acting on the C..."

## [1] "oxidoreductase activity"

## [1] "lyase activity"

## [1] "NAD binding"

## [1] "pyrophosphatase activity"

## [1] "NADP binding"

## [1] "protein binding"

## [1] "transporter activity"

## [1] "cysteine-type endopeptidase activity"

## [1] "iron ion binding"

BP Tcell vs RAG: BioGlyCMK
ontology <- 'BP'
GOdata.bac.enr <- new('topGOdata', ontology = ontology, allGenes = geneList.bac.enr, geneSel = topDiffGenes, annot = annFUN.gene2GO, gene2GO = gene2GOID)
result.bac.enr.ks <- runTest(GOdata.bac.enr, statistic = 'ks')
a <- GenTable(GOdata.bac.enr, result.bac.enr.ks, topNodes = 10)
kable(a)
| GO:0006520 |
cellular amino acid metabolic process |
140 |
0 |
0.65 |
7.7e-13 |
| GO:0055114 |
oxidation-reduction process |
369 |
2 |
1.72 |
7.6e-10 |
| GO:0006508 |
proteolysis |
19 |
0 |
0.09 |
7.4e-07 |
| GO:0006814 |
sodium ion transport |
18 |
0 |
0.08 |
2.0e-06 |
| GO:0006006 |
glucose metabolic process |
53 |
0 |
0.25 |
6.4e-06 |
| GO:0044267 |
cellular protein metabolic process |
35 |
0 |
0.16 |
2.5e-05 |
| GO:0042026 |
protein refolding |
19 |
0 |
0.09 |
0.00067 |
| GO:0005980 |
glycogen catabolic process |
4 |
0 |
0.02 |
0.00150 |
| GO:0006555 |
methionine metabolic process |
4 |
0 |
0.02 |
0.00462 |
| GO:0006177 |
GMP biosynthetic process |
3 |
0 |
0.01 |
0.00569 |
for (term in a$GO.ID){
print(a[a$GO.ID == term, ]$Term)
print(showGroupDensity(GOdata.bac.enr, term, ranks=TRUE))
}
## [1] "cellular amino acid metabolic process"

## [1] "oxidation-reduction process"

## [1] "proteolysis"

## [1] "sodium ion transport"

## [1] "glucose metabolic process"

## [1] "cellular protein metabolic process"

## [1] "protein refolding"

## [1] "glycogen catabolic process"

## [1] "methionine metabolic process"

## [1] "GMP biosynthetic process"

#showGroupDensity(GOdata.bac.enr, "GO:0006508", ranks = TRUE) #proteolysis
RAG vs TCell - BioGlyCMK
ontology <- 'MF'
MF
geneList.bac.enr <- -1*geneList.bac.enr
GOdata.bac.enr <- new('topGOdata', ontology = ontology, allGenes = geneList.bac.enr, geneSel = topDiffGenes, annot = annFUN.gene2GO, gene2GO = gene2GOID)
result.bac.enr.ks <- runTest(GOdata.bac.enr, statistic = 'ks')
a <- GenTable(GOdata.bac.enr, result.bac.enr.ks, topNodes = 10)
kable(a)
| GO:0050242 |
pyruvate, phosphate dikinase activity |
55 |
0 |
0.65 |
1.3e-25 |
| GO:0016301 |
kinase activity |
61 |
0 |
0.72 |
3.2e-19 |
| GO:0016903 |
oxidoreductase activity, acting on the a… |
141 |
0 |
1.66 |
9.1e-13 |
| GO:0051536 |
iron-sulfur cluster binding |
45 |
0 |
0.53 |
2.7e-11 |
| GO:0016887 |
ATPase activity |
33 |
0 |
0.39 |
9.0e-11 |
| GO:0005524 |
ATP binding |
149 |
0 |
1.75 |
4.7e-10 |
| GO:0004634 |
phosphopyruvate hydratase activity |
44 |
0 |
0.52 |
2.2e-08 |
| GO:0016820 |
hydrolase activity, acting on acid anhyd… |
16 |
0 |
0.19 |
6.8e-07 |
| GO:0000287 |
magnesium ion binding |
57 |
1 |
0.67 |
1.0e-05 |
| GO:0016747 |
transferase activity, transferring acyl … |
26 |
0 |
0.31 |
1.6e-05 |
for (term in a$GO.ID){
print(a[a$GO.ID == term, ]$Term)
print(showGroupDensity(GOdata.bac.enr, term, ranks=TRUE))
}
## [1] "pyruvate, phosphate dikinase activity"

## [1] "kinase activity"

## [1] "oxidoreductase activity, acting on the a..."

## [1] "iron-sulfur cluster binding"

## [1] "ATPase activity"

## [1] "ATP binding"

## [1] "phosphopyruvate hydratase activity"

## [1] "hydrolase activity, acting on acid anhyd..."

## [1] "magnesium ion binding"

## [1] "transferase activity, transferring acyl ..."

BP - RAG vs Tcell: BioGlyCMK
ontology <- 'BP'
GOdata.bac.enr <- new('topGOdata', ontology = ontology, allGenes = geneList.bac.enr, geneSel = topDiffGenes, annot = annFUN.gene2GO, gene2GO = gene2GOID)
result.bac.enr.ks <- runTest(GOdata.bac.enr, statistic = 'ks')
a <- GenTable(GOdata.bac.enr, result.bac.enr.ks, topNodes = 10)
kable(a)
| GO:0006090 |
pyruvate metabolic process |
132 |
4 |
1.54 |
1.2e-25 |
| GO:0016310 |
phosphorylation |
133 |
4 |
1.55 |
4.4e-25 |
| GO:0022900 |
electron transport chain |
16 |
0 |
0.19 |
2.9e-05 |
| GO:0005978 |
glycogen biosynthetic process |
4 |
0 |
0.05 |
0.00044 |
| GO:0006096 |
glycolytic process |
77 |
4 |
0.90 |
0.00046 |
| GO:0016226 |
iron-sulfur cluster assembly |
12 |
0 |
0.14 |
0.00054 |
| GO:0006730 |
one-carbon metabolic process |
7 |
0 |
0.08 |
0.00286 |
| GO:0006810 |
transport |
51 |
0 |
0.60 |
0.00352 |
| GO:0005975 |
carbohydrate metabolic process |
224 |
4 |
2.61 |
0.00414 |
| GO:0006091 |
generation of precursor metabolites and … |
116 |
4 |
1.35 |
0.00616 |
for (term in a$GO.ID){
print(a[a$GO.ID == term, ]$Term)
print(showGroupDensity(GOdata.bac.enr, term, ranks=TRUE))
}
## [1] "pyruvate metabolic process"

## [1] "phosphorylation"

## [1] "electron transport chain"

## [1] "glycogen biosynthetic process"

## [1] "glycolytic process"

## [1] "iron-sulfur cluster assembly"

## [1] "one-carbon metabolic process"

## [1] "transport"

## [1] "carbohydrate metabolic process"

## [1] "generation of precursor metabolites and ..."

#showGroupDensity(GOdata.bac.enr, "GO:0006091", ranks=TRUE) #generation of precursor metabolites
#showGroupDensity(GOdata.bac.enr, "GO:0006090", ranks=TRUE) # pyruvate metabolic process
Enriched vs Unenriched
groups <- read.csv(file.path(data.dir, 'groups.csv'))
groups.rt <- groups[groups$RT_Enriched == 'True' | groups$RT_Unenriched == 'True', ]
geneList.rt.enr <- groups.rt$RT_Enriched == 'True' & groups.rt$RT_Unenriched == 'False'
geneList.rt.enr <- as.numeric(geneList.rt.enr)
names(geneList.rt.enr) <- groups.rt$X
sigFunc <- function(score) {return(score > 0.5)}
MF - Enr vs Unenr: Tcell
ontology <- 'MF'
GOdata.rt.enr <- new('topGOdata', ontology = ontology, allGenes = geneList.rt.enr, geneSel = sigFunc, annot = annFUN.gene2GO, gene2GO = gene2GOID)
result.rt.enr.fisher <- runTest(GOdata.rt.enr, statistic = 'fisher')
kable(GenTable(GOdata.rt.enr, result.rt.enr.fisher, topNodes = 10))
| GO:0016620 |
oxidoreductase activity, acting on the a… |
146 |
76 |
30.70 |
1.2e-14 |
| GO:0004816 |
asparagine-tRNA ligase activity |
18 |
17 |
3.78 |
3.8e-11 |
| GO:0003824 |
catalytic activity |
2849 |
644 |
599.07 |
5.0e-08 |
| GO:0008234 |
cysteine-type peptidase activity |
23 |
19 |
4.84 |
3.4e-06 |
| GO:0046872 |
metal ion binding |
472 |
83 |
99.25 |
1.3e-05 |
| GO:0008774 |
acetaldehyde dehydrogenase (acetylating)… |
17 |
12 |
3.57 |
1.5e-05 |
| GO:0004197 |
cysteine-type endopeptidase activity |
15 |
11 |
3.15 |
2.0e-05 |
| GO:0004022 |
alcohol dehydrogenase (NAD) activity |
18 |
12 |
3.78 |
3.6e-05 |
| GO:0004375 |
glycine dehydrogenase (decarboxylating) … |
6 |
6 |
1.26 |
8.5e-05 |
| GO:0004825 |
methionine-tRNA ligase activity |
12 |
9 |
2.52 |
9.1e-05 |
BP - Enr vs Unenr: Tcell
ontology <- 'BP'
GOdata.rt.enr <- new('topGOdata', ontology = ontology, allGenes = geneList.rt.enr, geneSel = sigFunc, annot = annFUN.gene2GO, gene2GO = gene2GOID)
result.rt.enr.fisher <- runTest(GOdata.rt.enr, statistic = 'fisher')
kable(GenTable(GOdata.rt.enr, result.rt.enr.fisher, topNodes = 10))
| GO:0006421 |
asparaginyl-tRNA aminoacylation |
18 |
17 |
3.71 |
2.7e-11 |
| GO:0008152 |
metabolic process |
2834 |
603 |
583.98 |
1.0e-10 |
| GO:0015976 |
carbon utilization |
17 |
12 |
3.50 |
1.2e-05 |
| GO:0006508 |
proteolysis |
89 |
36 |
18.34 |
3.9e-05 |
| GO:0006431 |
methionyl-tRNA aminoacylation |
12 |
9 |
2.47 |
7.7e-05 |
| GO:0006066 |
alcohol metabolic process |
42 |
13 |
8.65 |
0.00014 |
| GO:0009082 |
branched-chain amino acid biosynthetic p… |
24 |
13 |
4.95 |
0.00028 |
| GO:0009081 |
branched-chain amino acid metabolic proc… |
29 |
18 |
5.98 |
0.00034 |
| GO:0006099 |
tricarboxylic acid cycle |
5 |
5 |
1.03 |
0.00037 |
| GO:0006546 |
glycine catabolic process |
8 |
7 |
1.65 |
0.00043 |
RAG Enr vs Unenr
groups.rag <- groups[groups$RAG_Enriched == 'True' | groups$RAG_Unenriched == 'True', ]
geneList.rag.enr <- groups.rag$RAG_Enriched == 'True' & groups.rag$RAG_Unenriched == 'False'
geneList.rag.enr <- as.numeric(geneList.rag.enr)
names(geneList.rag.enr) <- groups.rag$X
MF - Enr vs Unenr: RAG
ontology <- 'MF'
GOdata.rag.enr <- new('topGOdata', ontology = ontology, allGenes = geneList.rag.enr, geneSel = sigFunc, annot = annFUN.gene2GO, gene2GO = gene2GOID)
result.rag.enr.fisher <- runTest(GOdata.rag.enr, statistic = 'fisher')
kable(GenTable(GOdata.rag.enr, result.rag.enr.fisher, topNodes = 10))
| GO:0016620 |
oxidoreductase activity, acting on the a… |
142 |
77 |
29.01 |
4.7e-17 |
| GO:0004816 |
asparagine-tRNA ligase activity |
18 |
17 |
3.68 |
2.3e-11 |
| GO:0003824 |
catalytic activity |
2697 |
595 |
550.94 |
1.2e-08 |
| GO:0008774 |
acetaldehyde dehydrogenase (acetylating)… |
17 |
12 |
3.47 |
1.1e-05 |
| GO:0008234 |
cysteine-type peptidase activity |
22 |
18 |
4.49 |
1.3e-05 |
| GO:0004197 |
cysteine-type endopeptidase activity |
15 |
11 |
3.06 |
1.5e-05 |
| GO:0004022 |
alcohol dehydrogenase (NAD) activity |
18 |
12 |
3.68 |
2.6e-05 |
| GO:0004375 |
glycine dehydrogenase (decarboxylating) … |
6 |
6 |
1.23 |
7.1e-05 |
| GO:0004825 |
methionine-tRNA ligase activity |
12 |
9 |
2.45 |
7.2e-05 |
| GO:0004019 |
adenylosuccinate synthase activity |
8 |
7 |
1.63 |
9.5e-05 |
BP - Enr vs Unenr: RAG
ontology <- 'BP'
GOdata.rag.enr <- new('topGOdata', ontology = ontology, allGenes = geneList.rag.enr, geneSel = sigFunc, annot = annFUN.gene2GO, gene2GO = gene2GOID)
result.rag.enr.fisher <- runTest(GOdata.rag.enr, statistic = 'fisher')
kable(GenTable(GOdata.rag.enr, result.rag.enr.fisher, topNodes = 10))
| GO:0006421 |
asparaginyl-tRNA aminoacylation |
18 |
17 |
3.55 |
1.2e-11 |
| GO:0008152 |
metabolic process |
2674 |
547 |
527.01 |
3.8e-10 |
| GO:0015976 |
carbon utilization |
17 |
12 |
3.35 |
7.3e-06 |
| GO:0006508 |
proteolysis |
84 |
34 |
16.56 |
2.7e-05 |
| GO:0006431 |
methionyl-tRNA aminoacylation |
12 |
9 |
2.37 |
5.3e-05 |
| GO:0055114 |
oxidation-reduction process |
867 |
207 |
170.88 |
6.4e-05 |
| GO:0006066 |
alcohol metabolic process |
42 |
13 |
8.28 |
8.7e-05 |
| GO:0009082 |
branched-chain amino acid biosynthetic p… |
24 |
13 |
4.73 |
0.00017 |
| GO:0009081 |
branched-chain amino acid metabolic proc… |
28 |
17 |
5.52 |
0.00141 |
| GO:0006546 |
glycine catabolic process |
7 |
6 |
1.38 |
0.00146 |
Unenriched vs Enriched
geneList.rt.un <- groups.rt$RT_Enriched == 'False' & groups.rt$RT_Unenriched == 'True'
geneList.rt.un <- as.numeric(geneList.rt.un)
names(geneList.rt.un) <- groups.rt$X
MF - Unenr vs Enr: Tcell
ontology <- 'MF'
GOdata.rt.un <- new('topGOdata', ontology = ontology, allGenes = geneList.rt.un, geneSel = sigFunc, annot = annFUN.gene2GO, gene2GO = gene2GOID)
result.rt.un.fisher <- runTest(GOdata.rt.un, statistic = 'fisher')
kable(GenTable(GOdata.rt.un, result.rt.un.fisher, topNodes = 10))
| GO:0003735 |
structural constituent of ribosome |
153 |
132 |
47.98 |
< 1e-30 |
| GO:0005198 |
structural molecule activity |
298 |
246 |
93.44 |
< 1e-30 |
| GO:0003677 |
DNA binding |
137 |
111 |
42.96 |
< 1e-30 |
| GO:0003723 |
RNA binding |
216 |
145 |
67.73 |
< 1e-30 |
| GO:0032549 |
ribonucleoside binding |
861 |
279 |
269.98 |
< 1e-30 |
| GO:0003899 |
DNA-directed RNA polymerase activity |
137 |
107 |
42.96 |
1.7e-30 |
| GO:0004619 |
phosphoglycerate mutase activity |
44 |
40 |
13.80 |
1.4e-16 |
| GO:0046933 |
proton-transporting ATP synthase activit… |
32 |
30 |
10.03 |
1.4e-13 |
| GO:0016740 |
transferase activity |
869 |
284 |
272.49 |
0.00019 |
| GO:0003924 |
GTPase activity |
119 |
55 |
37.31 |
0.00039 |
BP - Unenr vs Enr: Tcell
ontology <- 'BP'
GOdata.rt.un <- new('topGOdata', ontology = ontology, allGenes = geneList.rt.un, geneSel = sigFunc, annot = annFUN.gene2GO, gene2GO = gene2GOID)
result.rt.un.fisher <- runTest(GOdata.rt.un, statistic = 'fisher')
kable(GenTable(GOdata.rt.un, result.rt.un.fisher, topNodes = 10))
| GO:0071973 |
bacterial-type flagellum-dependent cell … |
112 |
112 |
36.01 |
< 1e-30 |
| GO:0006412 |
translation |
261 |
173 |
83.92 |
< 1e-30 |
| GO:0006351 |
transcription, DNA-templated |
152 |
116 |
48.87 |
9.1e-30 |
| GO:0015986 |
ATP synthesis coupled proton transport |
34 |
30 |
10.93 |
1.3e-11 |
| GO:0000162 |
tryptophan biosynthetic process |
5 |
5 |
1.61 |
0.0034 |
| GO:0006438 |
valyl-tRNA aminoacylation |
5 |
5 |
1.61 |
0.0034 |
| GO:0006556 |
S-adenosylmethionine biosynthetic proces… |
84 |
39 |
27.01 |
0.0039 |
| GO:0015991 |
ATP hydrolysis coupled proton transport |
37 |
20 |
11.90 |
0.0045 |
| GO:0006801 |
superoxide metabolic process |
7 |
6 |
2.25 |
0.0056 |
| GO:0006563 |
L-serine metabolic process |
15 |
11 |
4.82 |
0.0066 |
RAG Unenriched vs Enriched
geneList.rag.un <- groups.rag$RAG_Enriched == 'False' & groups.rag$RAG_Unenriched == 'True'
geneList.rag.un <- as.numeric(geneList.rag.un)
names(geneList.rag.un) <- groups.rag$X
MF - Unenr vs Enr: RAG
ontology <- 'MF'
GOdata.rag.un <- new('topGOdata', ontology = ontology, allGenes = geneList.rag.un, geneSel = sigFunc, annot = annFUN.gene2GO, gene2GO = gene2GOID)
result.rag.un.fisher <- runTest(GOdata.rag.un, statistic = 'fisher')
kable(GenTable(GOdata.rag.un, result.rag.un.fisher, topNodes = 10))
| GO:0005198 |
structural molecule activity |
271 |
244 |
92.18 |
< 1e-30 |
| GO:0003735 |
structural constituent of ribosome |
139 |
124 |
47.28 |
< 1e-30 |
| GO:0003677 |
DNA binding |
136 |
111 |
46.26 |
< 1e-30 |
| GO:0032549 |
ribonucleoside binding |
835 |
285 |
284.04 |
2.2e-30 |
| GO:0003723 |
RNA binding |
202 |
146 |
68.71 |
8.6e-29 |
| GO:0003899 |
DNA-directed RNA polymerase activity |
136 |
107 |
46.26 |
1.3e-27 |
| GO:0004619 |
phosphoglycerate mutase activity |
43 |
42 |
14.63 |
3.7e-19 |
| GO:0046933 |
proton-transporting ATP synthase activit… |
33 |
31 |
11.23 |
5.6e-13 |
| GO:0016661 |
oxidoreductase activity, acting on other… |
23 |
22 |
7.82 |
6.8e-10 |
| GO:0003924 |
GTPase activity |
113 |
62 |
38.44 |
3.0e-06 |
BP - Unenr vs Enr: RAG
ontology <- 'BP'
GOdata.rag.un <- new('topGOdata', ontology = ontology, allGenes = geneList.rag.un, geneSel = sigFunc, annot = annFUN.gene2GO, gene2GO = gene2GOID)
result.rag.un.fisher <- runTest(GOdata.rag.un, statistic = 'fisher')
kable(GenTable(GOdata.rag.un, result.rag.un.fisher, topNodes = 10))
| GO:0071973 |
bacterial-type flagellum-dependent cell … |
112 |
112 |
38.53 |
< 1e-30 |
| GO:0006412 |
translation |
237 |
167 |
81.54 |
< 1e-30 |
| GO:0006351 |
transcription, DNA-templated |
149 |
114 |
51.26 |
2.2e-27 |
| GO:0015986 |
ATP synthesis coupled proton transport |
35 |
31 |
12.04 |
3.4e-11 |
| GO:0015991 |
ATP hydrolysis coupled proton transport |
32 |
21 |
11.01 |
0.00029 |
| GO:0006414 |
translational elongation |
56 |
31 |
19.27 |
0.00094 |
| GO:0000162 |
tryptophan biosynthetic process |
5 |
5 |
1.72 |
0.00479 |
| GO:0006801 |
superoxide metabolic process |
7 |
6 |
2.41 |
0.00812 |
| GO:0006563 |
L-serine metabolic process |
15 |
11 |
5.16 |
0.01086 |
| GO:0006556 |
S-adenosylmethionine biosynthetic proces… |
84 |
39 |
28.90 |
0.01385 |